Influence of DNA Extraction Kits on Freshwater Fungal DNA Metabarcoding

Overview

Journal PeerJ

Specialties Biology
Environmental Health
General Medicine

Date 2022 Jun 2

PMID 35651749

Authors

Shunsuke Matsuoka

Yoriko Sugiyama

Mariko Nagano

Hideyuki Doi

Affiliations

Soon will be listed here.

Abstract

Background: Environmental DNA (eDNA) metabarcoding is a common technique for efficient biodiversity monitoring, especially of microbes. Recently, the usefulness of aquatic eDNA in monitoring the diversity of both terrestrial and aquatic fungi has been suggested. In eDNA studies, different experimental factors, such as DNA extraction kits or methods, can affect the subsequent analyses and the results of DNA metabarcoding. However, few methodological studies have been carried out on eDNA of fungi, and little is known about how experimental procedures can affect the results of biodiversity analysis. In this study, we focused on the effect of DNA extraction method on fungal DNA metabarcoding using freshwater samples obtained from rivers and lakes.

Methods: DNA was extracted from freshwater samples using the DNeasy PowerSoil kit, which is mainly used to extractmicrobial DNA from soil, and the DNeasy Blood & Tissue kit, which is commonly used for eDNA studies on animals. We then compared PCR inhibition and fungal DNA metabarcoding results; operational taxonomic unit (OTU) number and composition of the extracted samples.

Results: No PCR inhibition was detected in any of the samples, and no significant differences in the number of OTUs and OTU compositions were detected between the samples processed using different kits. These results indicate that both DNA extraction kits may provide similar diversity results for the river and lake samples evaluated in this study. Therefore, it may be possible to evaluate the diversity of fungi using a unified experimental method, even with samples obtained for diversity studies on other taxa such as those of animals.

Citing Articles

The Use of eDNA Metabarcoding to Detect and Identify Phytophthora in Water Samples.

Randall E, Keillor B, Cooke D Methods Mol Biol. 2024; 2892:117-138.

PMID: 39729273 DOI: 10.1007/978-1-0716-4330-3_9.

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